Prion diseases are neurodegenerative disorders that appear to be caused by a conformational change in the prion protein (PrP), but high resolution structures of PrP or its fragments are not available. We combined low resolution structural prediction methods with all-atom molecular dynamics simulations in order to investigate the stability of the helical form of the 109-122 fragment (H1) of PrP. Mutation of residue Ala 117 to Val in this fragment leads to Gerstmann-Straussler-Scheinker syndrome (GSS), and we used computational methods to investigate the effects of mutations at this site on the stability of H1. Only the GSS causing mutation (Ala 117 -> Val) was helix destabilizing. We are currently extending these investigations to the complete PrP and investigating the stabilities in experimentally relevant mixed solvents. We constantly use the interactive graphics of MidasPlus to examine our structures and to prepare figures for publication. The ability of Midas to color code atoms and residues by different properties (mobility, hydrophobicity, charge etc.) is a valuable check of the calculations and gives an intuitive feeling for the energetics of the system. We have found our interactions with the staff at the Computer Graphics Laboratory to be especially valuable.